Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.77 kDa 
• Atom Count: 2429 
• Modelled Residue Count: 264 
• Deposited Residue Count: 298 
• Unique protein chains: 1

3UMW

Crystal structure of Pim1 kinase in complex with inhibitor (Z)-2-[(1H-indazol-3-yl)methylene]-6-methoxy-7-(piperazin-1-ylmethyl)benzofuran-3(2H)-one

• DOI: 10.2210/pdb3UMW/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2011-11-14 Released: 2012-10-03 
• Deposition Author(s): Parker, L.J., Handa, N., Yokoyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.200 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Rational evolution of a novel type of potent and selective proviral integration site in Moloney murine leukemia virus kinase 1 (PIM1) inhibitor from a screening-hit compound.

Nakano, H., Saito, N., Parker, L.J., Tada, Y., Abe, M., Tsuganezawa, K., Yokoyama, S., Tanaka, A., Kojima, H., Okabe, T., Nagano, T.

(2012) J Med Chem 55: 5151-5164

• PubMed: 22540945 
• DOI: 10.1021/jm3001289
• Primary Citation of Related Structures:  
  3UMW


• PubMed Abstract: 
  

Serine/threonine kinase PIM1 is an emerging therapeutic target for hematopoietic and prostate cancer therapy. To develop a novel PIM1 inhibitor, we focused on 1, a metabolically labile, nonselective kinase inhibitor discovered in our previous screening study. We adopted a rational optimization strategy based mainly on structural information for the PIM1-1 complex to improve the potency and selectivity. This approach afforded the potent and metabolically stable PIM1-selective inhibitor 14, which shows only a marginal increase in molecular weight compared with 1 but has a significantly decreased cLogP. The validity of our design concept was confirmed by X-ray structure analysis. In a cellular study, 14 potently inhibited the growth of human leukemia cell line MV4-11 but had a negligible effect on the growth of WI-38 (surrogate for general toxicity). These results demonstrate the effectiveness of our design strategy for evolving the screening-hit compound 1 into a novel type of PIM1 inhibitor, 14.

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Organizational Affiliation: 

Open Innovation Center for Drug Discovery, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase pim-1	A	298	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
596 (Subject of Investigation/LOI)	D [auth A]	(2Z)-2-(1H-indazol-3-ylmethylidene)-6-methoxy-7-(piperazin-1-ylmethyl)-1-benzofuran-3(2H)-one C22 H22 N4 O3 HZMQZYRYZGLOKJ-NDENLUEZSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
596	Binding MOAD:  3UMW	IC50: 3 (nM) from 1 assay(s)
	PDBBind:  3UMW	IC50: 3 (nM) from 1 assay(s)
	BindingDB:  3UMW	IC50: min: 3, max: 6 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.200 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.28	α = 90
b = 98.28	β = 90
c = 80.641	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2011-11-14 
• Released Date: 2012-10-03 
Deposition Author(s): Parker, L.J., Handa, N., Yokoyama, S.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release